Table 1 B. kashiwanohense APCKJ1 genes that are transcriptionally upregulated during growth in mMRS medium supplemented with 2′-FL as the sole carbohydrate, as compared to growth in mMRS supplemented with sorbitol.

Gene ID	Gene name	Function	2′-FL vs Sorbitol	2′-FL vs Lactose
BKKJ1_0067	BKKJ1_0067	ABC transporter substrate-binding protein	−8.12	—
BKKJ1_0068	BKKJ1_0068	ABC transporter permease	−5.91	—
BKKJ1_0069	BKKJ1_0069	ABC transporter permease	−5.71	—
BKKJ1_0206	BKKJ1_0206	6-phosphogluconate dehydrogenase	−13.31	—
BKKJ1_0207	BKKJ1_0207	hypothetical protein	−17.67	—
BKKJ1_0208	BKKJ1_0208	putative gluconokinase	−17.21	—
BKKJ1_0336	BKKJ1_0336	hypothetical protein	−16.99	—
BKKJ1_0338	BKKJ1_0338	hypothetical protein	−27.69	—
BKKJ1_0339	BKKJ1_0339	xylitol (sorbitol) dehydrogenase	−34.61	—
BKKJ1_0340	BKKJ1_0340	transcriptional regulator	−36.34	—
BKKJ1_0341	BKKJ1_0341	aldehyde-alcohol dehydrogenase 2	−22.03	—
BKKJ1_0429	fumG	L-1,2-propanediol oxidoreductase	—	5.90
BKKJ1_2066	lacS	galactoside symporter	—	5.35
BKKJ1_2067	lacA	beta-galactosidase	6.47	—
BKKJ1_2068	lacR	Truncated LacI-type transcriptional regulator	—	—
BKKJ1_2069	fumA1	GH95 alpha-1 3/4-fucosidase	7.45	6.88
BKKJ1_2070	fumA2	GH29 alpha-1 3/4-fucosidase	11.04	10.43
BKKJ1_2071	fumB	L-fucose mutarotase	12.80	12.17
BKKJ1_2072	fumF	L-2-keto-3-deoxy-fuconate aldolase	13.14	10.86
BKKJ1_2073	fumD	L-fuconolactone hydrolase	14.15	8.21
BKKJ1_2074	fumC	L-keto-3-deoxy-fuconate-4-dehydrogenase	15.95	15.37
BKKJ1_2075	fumE	L-fuconate dehydratase	17.29	13.90
BKKJ1_2076	fumS	ABC transporter solute binding protein	19.68	30.20
BKKJ1_2077	fumT1	ABC transporter permease	20.79	22.82
BKKJ1_2078	fumT2	ABC transporter permease	21.89	30.41
BKKJ1_2079	fumR	LacI family transcriptional regulator	—	—

The level of expression is shown as a fold-value of increase in expression on each carbohydrate, as compared to a sorbitol or lactose control, with a cut-off of a minimum 5.0-fold increase in expression. Microarray data were obtained using B. kashiwanohense APCKJ1 grown on 1% 2′-FL and were compared with array data obtained when B. kashiwanohense APCKJ1 was grown on sorbitol or lactose as a control. The cut-off point was set at 5.0-fold, with a P value of <0.001. With the - sign are indicated fold values below the cut-off. The predicted functions were determined using a combination of BLASTP⁷¹, Pfam (http://pfam.xfam.org) and KEGG (http://www.genome.jp/kegg/) searches.

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